Name: size matters: measurement of capsule diameter in cryptococcus neoformans
Uploaded: 2018-02-27T15:00:00
Description: Watch this Scientific Journal Video about Size Matters: Measurement of Capsule Diameter in Cryptococcus neoformans at JoVE.com

We thank the Molecular Biosciences (MOBI) doctoral program and the Biology Department at Middle Tennessee State University (MTSU) for providing the funding for this study. The project was also funded in part by a Special Projects grant awarded to D.E.N. by the MTSU Foundation.

NOTE: C. neoformans is a Biosafety Level 2 (BSL-2) pathogen and researchers working with it must take proper precautions. Detailed procedures on how to safely work with BSL-2 pathogens can be found on the Center for Disease Control&#39;s (CDC) website, but it is important to note that all persons coming into contact with C. neoformans should be properly trained in handling pathogenic agents and should always wear appropriate personal protective equipment (PPE), generally latex or nitrile gloves. Further...

<ol>
	<li>Park, B. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimation+of+the+current+global+burden+of+cryptococcal+meningitis+among+persons+living+with+HIV/AIDS.">Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS.</a> AIDS. 23 (4), 525-530 (2009).</li><li>Coelho, C., Bocca, A. L., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+intracellular+life+of+Cryptococcus+neoformans.">The intracellular life of Cryptococcus neoformans.</a> Annu Rev Pathol. 9, 219-238 (2014).</li><li>Rajasingham, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+burden+of+disease+of+HIV-associated+cryptococcal+meningitis:+an+updated+analysis.">Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis.</a> Lancet Infect Dis. 17 (8), 873-881 (2017).</li><li>Limper, A. H., Adenis, A., Le, T., Harrison, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fungal+infections+in+HIV/AIDS.">Fungal infections in HIV/AIDS.</a> Lancet Infect Dis. 17 (11), e334-e343 (2017).</li><li>Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crisis+in+Infectious+Diseases:+2+Decades+Later.">Crisis in Infectious Diseases: 2 Decades Later.</a> Clin Infect Dis. 64 (7), 823-828 (2017).</li><li>McClelland, E. E. C., Eisenmann, A., H, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch+6.">Ch 6.</a> New Insights in Medical Mycology. , 131-157 (2007).</li><li>Leopold Wager, C. M., Wormley, F. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Classical+versus+alternative+macrophage+activation:+the+Ying+and+the+Yang+in+host+defense+against+pulmonary+fungal+infections.">Classical versus alternative macrophage activation: the Ying and the Yang in host defense against pulmonary fungal infections.</a> Mucosal Immunol. 7 (5), 1023-1035 (2014).</li><li>Kwon-Chung, K. J., Rhodes, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Encapsulation+and+melanin+formation+as+indicators+of+virulence+in+Cryptococcus+neoformans.">Encapsulation and melanin formation as indicators of virulence in Cryptococcus neoformans.</a> Infect Immun. 51 (1), 218-223 (1986).</li><li>Vecchiarelli, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elucidating+the+immunological+function+of+the+Cryptococcus+neoformans+capsule.">Elucidating the immunological function of the Cryptococcus neoformans capsule.</a> Future Microbiol. 8 (9), 1107-1116 (2013).</li><li>Murphy, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+cryptococcal+antigens+on+cell-mediated+immunity.">Influence of cryptococcal antigens on cell-mediated immunity.</a> Rev Infect Dis. 10 Suppl 2, S432-S435 (1988).</li><li>Cherniak, R., Morris, L. C., Belay, T., Spitzer, E. D., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Variation+in+the+structure+of+glucuronoxylomannan+in+isolates+from+patients+with+recurrent+cryptococcal+meningitis.">Variation in the structure of glucuronoxylomannan in isolates from patients with recurrent cryptococcal meningitis.</a> Infect Immun. 63 (5), 1899-1905 (1995).</li><li>Collins, H. L., Bancroft, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Encapsulation+of+Cryptococcus+neoformans+impairs+antigen-specific+T-cell+responses.">Encapsulation of Cryptococcus neoformans impairs antigen-specific T-cell responses.</a> Infect Immun. 59 (11), 3883-3888 (1991).</li><li>Yasuoka, A., Kohno, S., Yamada, H., Kaku, M., Koga, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+molecular+sizes+of+Cryptococcus+neoformans+capsular+polysaccharide+on+phagocytosis.">Influence of molecular sizes of Cryptococcus neoformans capsular polysaccharide on phagocytosis.</a> Microbiol Immunol. 38 (11), 851-856 (1994).</li><li>Robertson, E. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cryptococcus+neoformans+ex+vivo+capsule+size+is+associated+with+intracranial+pressure+and+host+immune+response+in+HIV-associated+cryptococcal+meningitis.">Cryptococcus neoformans ex vivo capsule size is associated with intracranial pressure and host immune response in HIV-associated cryptococcal meningitis.</a> J Infect Dis. 209 (1), 74-82 (2014).</li><li>Cordero, R. J., Bergman, A., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temporal+behavior+of+capsule+enlargement+by+Cryptococcus+neoformans.">Temporal behavior of capsule enlargement by Cryptococcus neoformans.</a> Eukaryot Cell. 12 (10), 1383-1388 (2013).</li><li>O'Meara, T. R., Alspaugh, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cryptococcus+neoformans+capsule:+a+sword+and+a+shield.">The Cryptococcus neoformans capsule: a sword and a shield.</a> Clin Microbiol Rev. 25 (3), 387-408 (2012).</li><li>McClelland, E. E., Smith, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gender+specific+differences+in+the+immune+response+to+infection.">Gender specific differences in the immune response to infection.</a> Archivum Immunologiae et Therapiae Experimentalis. 59 (3), (2011).</li><li>McClelland, E. E., Perrine, W. T., Potts, W. K., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationship+of+virulence+factor+expression+to+evolved+virulence+in+mouse-passaged+Cryptococcus+neoformans+lines.">Relationship of virulence factor expression to evolved virulence in mouse-passaged Cryptococcus neoformans lines.</a> Infect Immun. 73 (10), 7047-7050 (2005).</li><li>Zaragoza, O., Fries, B. C., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+capsule+growth+in+Cryptococcus+neoformans+by+mammalian+serum+and+CO(2).">Induction of capsule growth in Cryptococcus neoformans by mammalian serum and CO(2).</a> Infect Immun. 71 (1), 6155-6164 (2003).</li><li>Vartivarian, S. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+cryptococcal+capsular+polysaccharide+by+iron.">Regulation of cryptococcal capsular polysaccharide by iron.</a> J Infect Dis. 167 (1), 186-190 (1993).</li><li>McFadden, D. C., Fries, B. C., Wang, F., Casadevall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capsule+structural+heterogeneity+and+antigenic+variation+in+Cryptococcus+neoformans.">Capsule structural heterogeneity and antigenic variation in Cryptococcus neoformans.</a> Eukaryot Cell. 6 (8), 1464-1473 (2007).</li><li>Garcia-Hermoso, D., Dromer, F., Janbon, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cryptococcus+neoformans+capsule+structure+evolution+in+vitro+and+during+murine+infection.">Cryptococcus neoformans capsule structure evolution in vitro and during murine infection.</a> Infect Immun. 72 (6), 3359-3365 (2004).</li><li>Gates, M. A., Thorkildson, P., Kozel, T. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+architecture+of+the+Cryptococcus+neoformans+capsule.">Molecular architecture of the Cryptococcus neoformans capsule.</a> Mol Microbiol. 52 (1), 13-24 (2004).</li><li>Pontes, B., Frases, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cryptococcus+neoformans+capsule:+lessons+from+the+use+of+optical+tweezers+and+other+biophysical+tools.">The Cryptococcus neoformans capsule: lessons from the use of optical tweezers and other biophysical tools.</a> Front Microbiol. 6, 640 (2015).</li><li>Shen, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+tracking+of+gene+expression+in+individual+cells+and+cell+compartments.">Automated tracking of gene expression in individual cells and cell compartments.</a> J R Soc Interface. 3 (11), 787-794 (2006).</li><li>Dorn, J. F., Danuser, G., Yang, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computational+processing+and+analysis+of+dynamic+fluorescence+image+data.">Computational processing and analysis of dynamic fluorescence image data.</a> Methods Cell Biol. 85, 497-538 (2008).</li><li>Nketia, T. A., Sailem, H., Rohde, G., Machiraju, R., Rittscher, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+live+cell+images:+Methods,+tools+and+opportunities.">Analysis of live cell images: Methods, tools and opportunities.</a> Methods. , 65-79 (2017).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Biosafety in Microbiological and Biomedical Laboratories. , 33-38 (2015).</li><li>Kwon, O., Kang, S. T., Kim, S. H., Kim, Y. H., Shin, Y. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maximum+intensity+projection+using+bidirectional+compositing+with+block+skipping.">Maximum intensity projection using bidirectional compositing with block skipping.</a> J Xray Sci Technol. 23 (1), 33-44 (2015).</li><li>Janbon, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+the+genome+and+transcriptome+of+Cryptococcus+neoformans+var.+grubii+reveals+complex+RNA+expression+and+microevolution+leading+to+virulence+attenuation.">Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.</a> PLoS Genet. 10 (4), e1004261 (2014).</li><li>Bisson, G. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+HAART+is+associated+with+decreased+risk+of+death+during+initial+treatment+of+cryptococcal+meningitis+in+adults+in+Botswana.">The use of HAART is associated with decreased risk of death during initial treatment of cryptococcal meningitis in adults in Botswana.</a> J Acquir Immune Defic Syndr. 49 (2), 227-229 (2008).</li><li>van Teeffelen, S., Shaevitz, J. W., Gitai, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+analysis+in+fluorescence+microscopy:+bacterial+dynamics+as+a+case+study.">Image analysis in fluorescence microscopy: bacterial dynamics as a case study.</a> Bioessays. 34 (5), 427-436 (2012).</li><li>Granger, D. L., Perfect, J. R., Durack, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Virulence+of+Cryptococcus+neoformans.+Regulation+of+capsule+synthesis+by+carbon+dioxide.">Virulence of Cryptococcus neoformans. Regulation of capsule synthesis by carbon dioxide.</a> J Clin Invest. 76 (2), 508-516 (1985).</li></ol>

For decades, the capsule has been a major focus of research for both mycologists and clinicians interested in C. neoformans and cryptococcosis due to its role as a major virulence factor for the pathogen. Using microscopy to measure differences in capsule size between strains and under different growth conditions can provide important information about the pathogen and its responses to various stimuli (i.e., different environmental conditions, potential drug treatments, etc.) Here, we have outl...

Affecting a quarter million people every year and resulting in more than 180,000 deaths annually, Cryptococcus neoformans is a pathogenic, intracellular yeast and the causative agent of cryptococcosis1,2,3. Hardest hit are HIV-positive patients in poor countries who do not have ready access to antiretroviral therapy, making them acutely susceptible to the illness4,5,6. Data from the CDC indicate that in sub-Saharan Africa, C. neoformans kills more people than tuberculosis annually and more every month than any Ebola outbreak on record1. The most common route of exposure occurs from inhaling desiccated spores that are commonplace in the environment7. Upon entering the lungs, there are several virulence factors that contribute to the success of C. neoformans within infected individuals. The polysaccharide capsule is considered the microbe&#39;s primary virulence factor, as acapsular strains are not virulent8.
The cryptococcal capsule is made of up three principle components: glucuronoxylomannan (GXM), galactoxylomannan (GalXM), and mannoproteins (MPs)9. While MPs are a relatively minor cell wall-associated component of the capsule, they are immunogenic and can promote a mostly pro-inflammatory response9,10. In contrast, GXM and GalXM make up the bulk of the capsule (&#62;90% by weight) and have immunosuppressive effects11. In addition to its immunomodulatory effects, the rapid enlargement of the capsule in vivo creates a mechanical barrier to ingestion by host phagocytic cells (i.e., neutrophils and macrophages)12. The C. neoformans capsule and its synthesis are complex, but overall, increased capsule diameter is correlated with increased virulence6,13,14. Given this, it is important for C. neoformans researchers to be able to quickly and accurately quantify capsule measurements.
Both the C. neoformans cell and its polysaccharide capsule are dynamic structures and show changes over time15. The capsule can change in density, size, and assembly in response to changes in the host environment16,17,18. Low iron or nutrient levels, exposure to serum, the human physiological pH, and increased CO2 are known to initiate capsule growth16,18,19,20. Further, researchers have shown structural changes resulting in significant differences in immunoreactivity during an infection, lending an advantage to C. neoformans over its host21,22. This is known because the architecture of the C. neoformans capsule has been analyzed in a variety of ways. Electron microscopy, for example, has revealed that the capsule has a heterogeneous matrix with an inner electron-dense layer underneath an outer, more permeable layer23. Light scattering and the use of optical tweezers have allowed researchers to further elucidate its macromolecular properties24. Analyzing the results from both static and dynamic light scattering measurements, we know that the polysaccharide capsule has a complex branching structure23. Optical tweezers have been used to test the rigidity of the structure as well as evaluate its antibody reactivity24. However, by far the most frequently employed analysis of the C. neoformans capsule is the measurement of its size.
To quantify capsule size, researchers use what should be a simple measurement: the linear diameter of the capsule. Digital microscopes are used to capture images of multiple C. neoformans cells (generally hundreds) stained with either India ink or fluorescent dyes. The size of each cell body and surrounding capsule is measured. The data are compiled, and the average diameter of the capsule is calculated by subtracting the cell body diameter from the whole cell diameter (cell body + capsule). Up until this point, these measurements have been done manually. While generally accurate, this method has drawbacks for researchers. Large data sets can take days or even weeks to analyze by hand. And because these measurements are done manually, subjectivity and human error may affect the result.
Automated computational image analysis has become an indispensable tool for researchers in many areas of molecular cell biology, enabling faster and more reliable analysis of biological images 25,26,27. Precise image analysis techniques are necessary to mine quantitative information from what are often complex and immense data sets. However, some measurements, especially the measurement of C. neoformans capsule, have been difficult to automate. Accurately identifying the interface between the cell wall and capsule, which generally appears as a dark ring when imaged by phase-contrast microscopy, can be troublesome to resolve using a simple threshold. Further, C. neoformans cells in culture tend to clump together and accurate segmentation of the cells is necessary for accurate measurements.
The aim of this project was to (i) illustrate one of the standard protocols for capsule induction in C. neoformans, (ii) compare and contrast India ink and fluorescence staining as they pertain to capsule diameter measurements, (iii) develop simple, computational methods to measure capsule diameter using images of India ink stained cells using an image analysis software, and, (iv) assess the benefits and limitations of measuring capsule diameter manually and using software automation. We find that of the two staining methods, fluorescent labeling of the cell wall and capsule, while more time-consuming, provided the most consistent results between experiments. However, both methods enabled us to successfully distinguish between lab and clinical C. neoformans strains exhibiting different capsule sizes. Further, we were able to automate the measurement of capsule diameter from India ink stained images and found that this was a viable alternative to manual measurement of capsule.

<table border="0" cellpadding="0" cellspacing="0" width="983">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:451px;">Capsule Induction</td>
			<td style="width:204px;"></td>
			<td style="width:117px;"></td>
			<td style="width:211px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">C. neoformans cells</td>
			<td></td>
			<td></td>
			<td>The clinical lab strain, H99S, was a kind gift from Dr. John Perfect (Duke University).&#160; The clinical strains, B18 and B52, were kind gifts from Dr. Greg Bisson (University of Pennsylania).&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Yeast Peptone Dextrose Broth (YPD)</td>
			<td>Fisher Scientific</td>
			<td>DF0428-17-5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phosphate Buffered Saline (PBS)</td>
			<td></td>
			<td></td>
			<td>This is made in the lab using standard recipe (137mM NaCl, 2.7 mM KCl, 10mM Na2HPO4O, 2 mM Kh2PO4O)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM/high-glucose with L-glutamine, without sodium pyruvate</td>
			<td>GE Life Sciences</td>
			<td>SH30022.01</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">6-well plates</td>
			<td>Falcon</td>
			<td>CL5335-5EA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Shaking incubator</td>
			<td>Thermo Scientific&#160;</td>
			<td></td>
			<td>MaxQ6000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">CO2 incubator</td>
			<td>Fisher Scientific</td>
			<td></td>
			<td>Isotemp</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Centrifuge</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td>Legend XTR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Staining</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Microcentrifuge</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td>Legend Micro 21R</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">India ink</td>
			<td>Fisher Scientific</td>
			<td>14-910-56</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Calcofluor white</td>
			<td>Sigma-Aldrich</td>
			<td>18909-100ML-F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">18B7 mouse anti-GXM antibody conjugated to Alexafluor 488</td>
			<td></td>
			<td></td>
			<td>A kind gift from Dr. Arturo Casadevall (Johns Hopkins University)&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PBS with 1% Bovine Serum Albumin (BSA)</td>
			<td></td>
			<td></td>
			<td>PBS is the same recipe listed above (line 4) with 1% BSA added and filter sterilized.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bovine Serum Albumin</td>
			<td>Sigma-Aldrich</td>
			<td>A9418</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Superfrost microscope slides</td>
			<td>Fisher Scientific</td>
			<td>12-550-143</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glass coverslips</td>
			<td>Corning</td>
			<td>2855-18</td>
			<td>#1.5 thickness</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Clear nail polish or other non-toxic sealant</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Image Acquisition&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Immersion oil</td>
			<td>Cargille&#160;</td>
			<td>16484</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Light microscope with immersion oil objective</td>
			<td>Zeiss</td>
			<td></td>
			<td>Zeiss Axio A1 with a Plan - NEOFLUAR 100x oil immersion NA 1.30 objective</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Light microscope camera</td>
			<td>Zeiss</td>
			<td></td>
			<td>Zeiss Axiocam ErCD camera</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Confocal microscope with oil immersion objective</td>
			<td>Zeiss</td>
			<td></td>
			<td>LSM 700 laser scanning confocal equipped with a Plan-Apochromat 63X NA 1.4 oil immersion DIC M27 objective.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Confocal microscope software</td>
			<td>Zen 2009</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Confocal microscope camera</td>
			<td>Nikon</td>
			<td></td>
			<td>Nikon Ti-Eclipse with a Intensilight epifluorescence illuminator (Nikon), CoolSNAP MYO microscope camera (Photometrics), Plan Apo 60x NA 1.40 oil immersion objective (Nikon) and 1.5x magnification changer.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Widefield imaging software</td>
			<td>Nikon Elements (Nikon)</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Capsule Measurement</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Image editing software</td>
			<td>Photoshop (Adobe)</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Microscope software for manual measurement</td>
			<td>Axiovision (Carl Zeiss)</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Image analysis software for automated meesurement</td>
			<td>Aivia (DRVision Technologies)</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Spreadsheet software</td>
			<td>Excel (Microsoft)</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

size matters: measurement of capsule diameter in cryptococcus neoformans

The polysaccharide capsule of Cryptococcus neoformans is the primary virulence factor and one of the most commonly studied aspects of this pathogenic yeast. Capsule size can vary widely between strains, has the ability to grow rapidly when introduced to stressful or low nutrient conditions, and has been positively correlated with strain virulence. For these reasons, the size of the capsule is of great interest to C. neoformans researchers. The growth of the C. neoformans capsule is induced during phenotypic testing to help understand the effects of different treatments on the yeast or size differences between strains. Here we describe one of the standard methods of capsule induction and compare two accepted methods of staining and measuring capsule diameter: (i) India ink, a negative stain, used in conjunction with conventional light microscopy and (ii) co-staining with fluorescent dyes of both the cell wall and capsule followed by confocal microscopy. Finally, we show how measurement of capsule diameter from India ink-stained samples can be automated using computational image analysis.

To illustrate capsule induction, cell staining, imaging, and measuring techniques, we used three strains of C. neoformans: the common, well-characterized laboratory strain, H99S30, and two clinically isolated strains of previously unknown capsule diameter, B18 and B5231.
The workflow of capsule induction, staining, and image acquisition using India ink is shown in <strong ...

Watch this Scientific Journal Video about Size Matters: Measurement of Capsule Diameter in Cryptococcus neoformans at JoVE.com

Size Matters: Measurement of Capsule Diameter in Cryptococcus neoformans

The polysaccharide capsule is the primary virulence factor in Cryptococcus neoformans, and its size correlates with strain virulence. Capsule diameter measurements are used in phenotypic testing and to gauge therapeutic efficacy. Here a standard method of capsule induction is presented, and two methods of staining and measuring diameter are compared.

Size Matters: Measurement of Capsule Diameter in Cryptococcus neoformans

The polysaccharide capsule of Cryptococcus neoformans is the primary virulence factor and one of the most commonly studied aspects of this pathogenic ...

The overall goal of this procedure is to stain the polysaccharide capsule of C.neoformans strains for the visualization and measurement of the capsule diameter. These methods can help researchers with the induction, imaging, and measurement of capsule size in Cryptococcus neoformans. The main advantage of the staining and imaging techniques is that they are simple, fast, and allow for an accurate measurement of capsule diameter.Visual demonstration of this method is critical as the software steps may be confusing the first time it is used. Diameter of the Cryptococcus neoformans'capsule is often used as a measure of virulence. The ability to automate this process can save significant analysis time.To induce capsule production, first incubate a C.neoformans colony in yeast peptone dextrose broth at 37 degrees Celsius with shaking for 18-36 hours until the culture is in log phase. At the end of the culture, pellet the yeast by centrifugation and wash the yeast three times in PBS. After the last wash, resuspend the yeast at two times 10 to the fifth cells per two milliliters of DMEM concentration and incubate the culture at 37 degrees Celsius and 5%carbon dioxide for 18 hours.The next day, collect the cells by centrifugation and remove all but the last 10 microliters of the supernatant. To stain the yeast with India ink, resuspend the pellet in the remaining supernatant and transfer four microliters of the cell suspension and four microliters of India ink onto a glass microscope slide. Gently mix the resulting solution without creating bubbles.Then place a number 1.5 thickness 13 millimeter glass coverslip over the cell sample and seal the edges with a nontoxic sealant. To stain the yeast with a fluorescent dye, resuspend the overnight culture pellet in 50 microliters of PBS supplemented with 1%bovine serum and incubate the cells in 55-60 microliters of calcofluor-white and Alexa Fluor 488 conjugated capsule monoclonal 18B7 antibody for 30 minutes at 37 degrees Celsius. At the end of the incubation, collect the cells by centrifugation and resuspend the pellet in 10 microliters of PBS plus bovine serum albumin.Then transfer eight microliters of cells onto a glass microscope slide, cover the cell sample with a number 1.5 thickness 13 millimeter glass coverslip and seal the edges with a nontoxic sealant. To stain the yeast with both dyes, first incubate the cells with a fluorescent capsule and cell wall stain as just demonstrated. Then add four microliters of fluorescently-stained cells and four microliters of India ink onto a glass slide and place a sealed coverslip over the fungal cell sample as demonstrated.To image the cells by light microscopy, select the 100X objective and image at least 50 non-overlapping cells per condition with exposure times optimized to maximize the image contrast while minimizing the blur caused by small cell movements. To image the cells by fluorescence microscopy, open the microscope imaging software and select the appropriate excitation and emission wavelengths for the fluorophores used. In the Z stack control panel, select the first last option.Using the fine focus control on the microscope, first focus below the widest point of the cell body of a single yeast cell and the capsules for all of the cells within the current field of view and click set first. Next, use the fine focus control to focus above the widest point of the cell body of the same cell and of the capsule for all of the cells within the current field of view and click set last. Then open the acquisition tab and click start experiment to acquire the Z stack for the current position.To manually measure the capsule and cell diameters, open an appropriate cell measurement program and select the image to be measured. Select measure and use the cursor to draw a straight line through the widest point of the whole cell to measure the total cell diameter. Click measure again and draw a straight line through the cell body to measure the cell body diameter and open the next cell.When all of the cells have been measured, save the images. For automated measurement of the capsule and cell diameters, first open an appropriate image editing program and invert all of the India ink stained cell images. Next, to import both the original and inverted images into the cell measurement software, open the file menu in the measurement program and select import sequence, load image, define sequence manually, dimensions channel, import, and apply.To detect and mask the cell body, select the colony analyzer fluorescence protocol for the first inverted image of interest and click apply. Select the colony analyzer fluorescence protocol again to segment the inverted C.neoformans cell body images from their capsules and click apply again to create a count mask. Right click to rename the count mask cell body and use the cell proliferation protocol on the original image to detect and mask the capsule.Click apply to create a count mask for the original image and rename the count mask capsule. To create a new mask over the original image to partition the adjacent capsules from one another, select capsule partition and capsule for the capsule region. To export the data, click on spreadsheet then click on the export to spreadsheet icon.Select the measurements that you wish to export and then finally save the data. A capsule size increase is apparent in most strains post-induction, although some strains exhibit naturally small capsules. In this representative experiment, a significant difference in capsule size was consistently observed between the largest strain and the two smaller strains.Differences in capsule size can also be detected using fluorescent dyes. Z stack image capture ensures that the maximum capsule and cell body diameter is acquired for each cell. The stacks can then be processed to produce maximum intensity projections for the manual measurement of the yeast cell capsule and cell diameter.There is no significant intra-experiment difference between capsule measurements using either staining method, although a greater inter-experiment variability is observed when using India ink to measure capsule diameters compared to fluorescent dye staining. Significant differences in capsule diameter measurements between different researchers are not typically observed regardless of the method used while small but significant differences in the capsule size can be detected using the automated measurement method. For successful automated measuring, the cells must be in focus, have a medium to large capsule, and not be overly clustered.After watching this video, you should have a good understanding of how to induce the capsule in Cryptococcus neoformans, stain it using either India ink or fluorescent staining, image the capsule, and measure it via automated software.

size-matters-measurement-capsule-diameter-cryptococcus

Research

JoVE Journal

Immunology and Infection

Measurement of Cytosolic Ca2+ in Isolated Contractile Lymphatics

Lymphatic vessels comprise a multifunctional transport system that maintains fluid homeostasis, delivers lipids to the central circulation, and acts as a surveillance system for potentially harmful antigens, optimizing mucosal immunity and adaptive immune responses1. Lymph is formed from interstitial fluid that enters blind-ended initial lymphatics, and then is transported against a pressure gradient in larger collecting lymphatics. Each collecting lymphatic is made up of a series of segments called lymphangions, separated by bicuspid valves that prevent backflow. Each lymphangion possesses a contractile cycle that propels lymph against a pressure gradient toward the central circulation2. This phasic contractile pattern is analogous to the cardiac cycle, with systolic and diastolic phases, and with a lower contraction frequency4. In addition, lymphatic smooth muscle generates tone and displays myogenic constriction and dilation in response to increases and decreases in luminal pressure, respectively5. A hybrid of molecular mechanisms that support both the phasic and tonic contractility of lymphatics are thus proposed.
Contraction of smooth muscle is generally regulated by the cytosolic Ca2+ concentration ([Ca2+]i) plus sensitivity to Ca2+, of the contractile elements in response to changes in the environment surrounding the cell6. [Ca2+]i is determined by the combination of the movement of Ca2+ through plasma membrane ligand or voltage gated Ca2+ channels and the release and uptake of Ca2+ from internal stores. Cytosolic Ca2+ binds to calmodulin and activates enzymes such as myosin light chain (MLC) kinase (MLCK), which in turn phosphorylates MLC leading to actin-myosin-mediated contraction8. However, the sensitivity of this pathway to Ca2+ can be regulated by the MLC phosphatase (MLCP)9. MLCP activity is regulated by Rho kinase (ROCK) and the myosin phosphatase inhibitor protein CPI-17.
Here, we present a method to evaluate changes in [Ca2+]i over time in isolated, perfused lymphatics in order to study Ca2+-dependent and Ca2+-sensitizing mechanisms of lymphatic smooth muscle contraction. Using isolated rat mesenteric collecting lymphatics we studied stretch-induced changes in [Ca2+]i and contractile activity. The isolated lymphatic model offers the advantage that pressure, flow, and the chemical composition of the bath solution can be tightly controlled. [Ca2+]i was determined by loading lymphatics with the ratiometric, Ca2+-binding dye Fura-2. These studies will provide a new approach to the broader problem of studying the different molecular mechanisms that regulate phasic contractions versus tonic constriction in lymphatic smooth muscle.

Measurement of Cytosolic Ca2+ in Isolated Contractile Lymphatics

We introduce an approach to evaluate the cytosolic Ca2+ concentration in isolated lymphatics to study Ca2+-dependent and Ca2+-sensitizing mechanisms of lymphatic smooth muscle contraction.

Lymphatic vessels comprise a multifunctional transport system that maintains fluid homeostasis, delivers lipids to the central circulation, and acts as a ...

Measurement of &#947;HV68 Infection in Mice

&gamma;-Herpesviruses (&gamma;-HVs) are notable for their ability to establish latent infections of lymphoid cells1. The narrow host range of human &gamma;-HVs, such as EBV and KSHV, has severely hindered detailed pathogenic studies. Murine &gamma;-herpesvirus 68 (&gamma;HV68) shares extensive genetic and biological similarities with human &gamma;-HVs and is a natural pathogen of murid rodents2. As such, evaluation of &gamma;HV68 infection of mice inbred strains at different stages of viral infection provides an important model for understanding viral lifecycle and pathogenesis during &gamma;-HVs infection.
Upon intranasal inoculation, &gamma;HV68 infection results in acute viremia in the lung that is later resolved into a latent infection of splenocytes and other cells, which may be reactivated throughout the life of the host3,4. In this protocol, we will describe how to use the plaque assay to assess infectious virus titer in the lung homogenates on Vero cell monolayers at the early stage (5 - 7 days) of post-intranasal infection (dpi). While acute infection is largely cleared 2 - 3 weeks postinfection, a latent infection of &gamma;HV68 is established around 14 dpi and maintained later on in the spleen of the mice. Latent infection usually affects a very small population of cells in the infected tissues, whereby the virus stays dormant and shuts off most of its gene expression. Latently-infected splenocytes spontaneously reactivate virus upon explanting into tissue culture, which can be recapitulated by an infectious center (IC) assay to determine the viral latent load. To further estimate the amount of viral genome copies in the acutely and/or latently infected tissues, quantitative real-time PCR (qPCR) is used for its maximal sensitivity and accuracy. The combined analyses of the results of qPCR and plaque assay, and/or IC assay will reveal the spatiotemporal profiles of viral replication and infectivity in vivo.

Measurement of &amp;#947;HV68 Infection in Mice

&#947;-Herpesviruses (&#947;-HVs) establish life-long persistency in their host. Infection of mice with &#947;-HV68 provides a genetically tractable in vivo model for the characterization of the lifecycle/pathogenesis of &#947;HVs. This protocol describes the detection and quantitation of &#947;HV68 infection at acute and latent stages following infection by plaque-forming, infectious center, and qPCR assays.

&gamma;-Herpesviruses (&gamma;-HVs) are notable for their ability to establish latent infections of lymphoid cells1. The narrow host range of human ...

Quantitative Measurement of the Immune Response and Sleep in Drosophila

A complex interaction between the immune response and host behavior has been described in a wide range of species. Excess sleep, in particular, is known to occur as a response to infection in mammals 1 and has also recently been described in Drosophila melanogaster2. It is generally accepted that sleep is beneficial to the host during an infection and that it is important for the maintenance of a robust immune system3,4. However, experimental evidence that supports this hypothesis is limited4, and the function of excess sleep during an immune response remains unclear. We have used a multidisciplinary approach to address this complex problem, and have conducted studies in the simple genetic model system, the fruitfly Drosophila melanogaster. We use a standard assay for measuring locomotor behavior and sleep in flies, and demonstrate how this assay is used to measure behavior in flies infected with a pathogenic strain of bacteria. This assay is also useful for monitoring the duration of survival in individual flies during an infection. Additional measures of immune function include the ability of flies to clear an infection and the activation of NF&kappa;B, a key transcription factor that is central to the innate immune response in Drosophila. Both survival outcome and bacterial clearance during infection together are indicators of resistance and tolerance to infection. Resistance refers to the ability of flies to clear an infection, while tolerance is defined as the ability of the host to limit damage from an infection and thereby survive despite high levels of pathogen within the system5. Real-time monitoring of NF&kappa;B activity during infection provides insight into a molecular mechanism of survival during infection. The use of Drosophila in these straightforward assays facilitates the genetic and molecular analyses of sleep and the immune response and how these two complex systems are reciprocally influenced.

Quantitative Measurement of the Immune Response and Sleep in Drosophila

To understand a link between the immune response and behavior, we describe a method to measure locomotor behavior in Drosophila during bacterial infection as well as the ability of flies to mount an immune response by monitoring survival, bacterial load, and real-time activity of a key regulator of innate immunity, NF&kappa;B.

A complex interaction between the immune response and  host behavior has been described in a wide range of species. Excess sleep, in  particular, is known ...

Measurement of Tactile Allodynia in a Murine Model of Bacterial Prostatitis

Uropathogenic Escherichia coli (UPEC) are pathogens that play an important role in urinary tract infections and bacterial prostatitis1. We have recently shown that UPEC have an important role in the initiation of chronic pelvic pain2, a feature of Chronic prostatitis/Chronic pelvic pain syndrome (CP/CPPS)3,4. Infection of the prostate by clinically relevant UPEC can initiate and establish chronic pain through mechanisms that may involve tissue damage and the initiation of mechanisms of autoimmunity5.
A challenge to understanding the pathogenesis of UPEC in the prostate is the relative inaccessibility of the prostate gland to manipulation. We utilized a previously described intraurethral infection method6 to deliver a clinical strain of UPEC into male mice thereby establishing an ascending infection of the prostate. Here, we describe our protocols for standardizing the bacterial inoculum7 as well as the procedure for catheterizing anesthetized male mice for instillation of bacteria.
CP/CPPS is primarily characterized by the presence of tactile allodynia4. Behavior testing was based on the concept of cutaneous hyperalgesia resulting from referred visceral pain8-10. An irritable focus in visceral tissues reduces cutaneous pain thresholds allowing for an exaggerated response to normally non-painful stimuli (allodynia). Application of normal force to the skin result in abnormal responses that tend to increase with the intensity of the underlying visceral pain. We describe methodology in NOD/ShiLtJ mice that utilize von Frey fibers to quantify tactile allodynia over time in response to a single infection with UPEC bacteria.

Infection of the prostate may be a contributing factor in mediating pelvic pain in chronic prostatitis. We describe the procedure for preparation of standardized bacterial inoculum, instillation of bacteria into the urethra of male mice and methodology for measuring tactile allodynia in mice over time.

Uropathogenic Escherichia coli (UPEC) are pathogens that play an important role in urinary tract infections and bacterial prostatitis1. We have recently ...

Visualizing Non-lytic Exocytosis of Cryptococcus neoformans from Macrophages Using Digital Light Microscopy

Many aspects of the infection of macrophages by Cryptococcus neoformans have been extensively studied and well defined. However, one particular interaction that is not clearly understood is non-lytic exocytosis. In this process, yeast cells are released into the extracellular space by a poorly understood mechanism that leaves both the macrophage and Cn viable. Here, we describe how to follow a large number of individually infected macrophages for a 24 hr infection period by time-lapsed microscopy. Infected macrophages are housed in a heating chamber with a CO2 atmosphere attached to a microscope that provides the same conditions as a cell-culture incubator. Live digital microscopy can provide information about the dynamic interactions between a host and pathogen that is not available from static images. Being able to visualize each infected cell can provide clues as to how macrophages handle fungal infections, and vice versa. This technique is a powerful tool in studying the dynamics that are behind a complex phenomenon.

Visualizing Non-lytic Exocytosis of Cryptococcus neoformans from Macrophages Using Digital Light Microscopy

We describe how to visualize macrophage-C. neoformans (Cn) interactions in real time, with specific emphasis on the process of non-lytic exocytosis using digital light microscopy. Using this technique individually infected macrophages can be studied to ascertain various aspects of this phenomenon.

Many aspects of the infection of macrophages by Cryptococcus neoformans have been extensively studied and well defined. However, one particular ...

Macrophage Cholesterol Depletion and Its Effect on the Phagocytosis of Cryptococcus neoformans

Cryptococcosis is a life-threatening infection caused by pathogenic fungi of the genus Cryptococcus. Infection occurs upon inhalation of spores, which are able to replicate in the deep lung. Phagocytosis of Cryptococcus by macrophages is one of the ways that the disease is able to spread into the central nervous system to cause lethal meningoencephalitis. Therefore, study of the association between Cryptococcus and macrophages is important to understanding the progression of the infection. The present study describes a step-by-step protocol to study macrophage infectivity by C. neoformansin vitro. Using this protocol, the role of host sterols on host-pathogen interactions is studied. Different concentrations of methyl--cyclodextrin (MCD) were used to deplete cholesterol from murine reticulum sarcoma macrophage-like cell line J774A.1. Cholesterol depletion was confirmed and quantified using both a commercially available cholesterol quantification kit and thin layer chromatography. Cholesterol depleted cells were activated using Lipopolysacharide (LPS) and Interferon gamma (IFN&#947;) and infected with antibody-opsonized Cryptococcus neoformans wild-type H99 cells at an effector-to-target ratio of 1:1. Infected cells were monitored after 2 hr of incubation with C. neoformans and their phagocytic index was calculated. Cholesterol depletion resulted in a significant reduction in the phagocytic index. The presented protocols offer a convenient method to mimic the initiation of the infection process in a laboratory environment and study the role of host lipid composition on infectivity.

Macrophage Cholesterol Depletion and Its Effect on the Phagocytosis of Cryptococcus neoformans

In this article, a protocol for infection of macrophages with Cryptococcus neoformans is described. Also, a method for sterol depletion from the macrophages is explained. These protocols provide a guide to study fungal infections in vitro and examine the role of sterols in such infections.

Cryptococcosis is a life-threatening infection caused by pathogenic fungi of the genus Cryptococcus. Infection occurs upon inhalation of spores, which are ...

Biolistic Transformation of a Fluorescent Tagged Gene into the Opportunistic Fungal Pathogen Cryptococcus neoformans

The basidiomycete Cryptococcus neoformans, an invasive opportunistic pathogen of the central nervous system, is the most frequent cause of fungal meningitis worldwide resulting in more than 625,000 deaths per year worldwide.&#160;Although electroporation has been developed for the transformation of plasmids in Cryptococcus, only&#160;biolistic&#160;delivery provides&#160;an effective means to transform&#160;linear&#160;DNA&#160;that can be integrated into the genome by homologous recombination.&#160;
Acetate has been shown to be a major fermentation product during cryptococcal infection, but the significance of this is not yet known.&#160;A bacterial pathway composed of the enzymes xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (Xfp) and acetate kinase (Ack) is one of three potential pathways for acetate production in C. neoformans. Here, we demonstrate the biolistic transformation of a construct, which has the gene encoding Ack fused to the fluorescent tag mCherry, into&#160;C. neoformans. We then confirm integration of the ACK-mCherry fusion into the&#160;ACK&#160;locus.

Biolistic Transformation of a Fluorescent Tagged Gene into the Opportunistic Fungal Pathogen Cryptococcus neoformans

Biolistic transformation is a method used to generate stable integration of DNA into the genome of the opportunistic pathogen Cryptococcus neoformans through homologous recombination. We will demonstrate biolistic transformation of a construct, which has the gene encoding acetate kinase fused to the fluorescent tag mCherry into&#160;C. neoformans.

The basidiomycete Cryptococcus neoformans, an invasive opportunistic pathogen of the central nervous system, is the most frequent cause of fungal ...

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

HIV-1 envelope proteins engage cognate receptors on the target cell surface, which leads to viral-cell membrane fusion followed by the release of the viral capsid (CA) core into the cytoplasm. Subsequently, the viral Reverse Transcriptase (RT), as part of a namesake nucleoprotein complex termed the Reverse Transcription Complex (RTC), converts the viral single-stranded RNA genome into a double-stranded DNA copy (vDNA). This leads to the biogenesis of another nucleoprotein complex, termed the pre-integration complex (PIC), composed of the vDNA and associated virus proteins and host factors. The PIC-associated viral integrase (IN) orchestrates the integration of the vDNA into the host chromosomal DNA in a temporally and spatially regulated two-step process. First, the IN processes the 3&#39; ends of the vDNA in the cytoplasm and, second, after the PIC traffics to the nucleus, it mediates integration of the processed vDNA into the chromosomal DNA. The PICs isolated from target cells acutely infected with HIV-1 are functional in vitro, as they are competent to integrate the associated vDNA into an exogenously added heterologous target DNA. Such PIC-based in vitro integration assays have significantly contributed to delineating the mechanistic details of retroviral integration and to discovering IN inhibitors. In this report, we elaborate upon an updated HIV-1 PIC assay that employs a nested real-time quantitative Polymerase Chain Reaction (qPCR)-based strategy for measuring the in vitro integration activity of isolated native PICs.

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

This report describes an in vitro assay for measuring the human immunodeficiency virus type 1 (HIV-1) preintegration complex (PIC)-associated integration activity in the cytoplasmic extracts of acutely infected cells. The integration of PIC-associated HIV-1 DNA into heterologous target DNA is quantified by using a nested real-time polymerase chain reaction strategy.

HIV-1 envelope proteins engage cognate receptors on the target cell surface, which leads to viral-cell membrane fusion followed by the release of the ...

Automated Measurement of Cryptococcal Species Polysaccharide Capsule and Cell Body

The purpose of this technique is to provide a consistent, accurate, and manageable process for large numbers of polysaccharide capsule measurements.
First, a threshold image is generated based on intensity values uniquely calculated for each image. Then, circles are detected based on contrast between the object and background using the well-established Circle Hough Transformation (CHT) algorithm. Finally, the detected cell capsules and bodies are matched according to center coordinates and radius size, and data is exported to the user in a manageable spreadsheet.
The advantages of this technique are simple but significant. First, because these calculations are performed by an algorithm rather than a human both accuracy and reliability are increased. There is no decline in accuracy or reliability regardless of how many samples are analyzed. Second, this approach establishes a potential standard operating procedure for the Cryptococcus field instead of the current situation where capsule measurement varies by lab. Third, given that manual capsule measurements are slow and monotonous, automation allows rapid measurements on large numbers of yeast cells that in turn facilitates high throughput data analysis and increasingly powerful statistics.
The major limitations of this technique come from how the algorithm functions. First, the algorithm will only generate circles. While Cryptococcus cells and their capsules take on a circular morphology, it would be difficult to apply this technique to non-circular object detection. Second, due to how circles are detected the CHT algorithm can detect enormous pseudo-circles based on the outer edges of several clustered circles. However, any misrepresented cell bodies caught within the pseudo-circle can be easily detected and removed from the resulting data sets.
This technique is meant for measuring the circular polysaccharide capsules of Cryptococcus species based on India Ink bright field microscopy; though it could be applied to other contrast based circular object measurements.

Automated Measurement of Cryptococcal Species Polysaccharide Capsule and Cell Body

This technique describes an automated batch image processor designed to measure polysaccharide capsule and body radii. While initially designed for Cryptococcus neoformans capsule measurements the automated image processor can also be applied to other contrast based detection of circular objects.

The purpose of this technique is to provide a consistent, accurate, and manageable process for large numbers of polysaccharide capsule measurements.
...

Complementary Use of Microscopic Techniques and Fluorescence Reading in Studying Cryptococcus-Amoeba Interactions

To simulate Cryptococcus infection, amoeba, which is the natural predator of cryptococcal cells in the environment, can be used as a model for macrophages. This predatory organism, similar to macrophages, employs phagocytosis to kill internalized cells. With the aid of a confocal laser-scanning microscope, images depicting interactive moments between cryptococcal cells and amoeba are captured. The resolution power of the electron microscope also helps to reveal the ultrastructural detail of cryptococcal cells when trapped inside the amoeba food vacuole. Since phagocytosis is a continuous process, quantitative data is then integrated in the analysis to explain what happens at the timepoint when an image is captured. To be specific, relative fluorescence units are read in order to quantify the efficiency of amoeba in internalizing cryptococcal cells. For this purpose, cryptococcal cells are stained with a dye that makes them fluoresce once trapped inside the acidic environment of the food vacuole. When used together, information gathered through such techniques can provide critical information to help draw conclusions on the behavior and fate of cells when internalized by amoeba and, possibly, by other phagocytic cells.

Complementary Use of Microscopic Techniques and Fluorescence Reading in Studying Cryptococcus-Amoeba Interactions

This paper details a protocol for preparing a co-culture of cryptococcal cells and amoebae that is studied using still, fluorescent images and high-resolution transmission electron microscope images. Illustrated here is how quantitative data can complement such qualitative information.